Does selling on an affiliate site affect my earnings on my own website?

[LetItMatter]

I am currently working with a company and synced with their app to sell my products on their website. They take a cut of the sales. 

I also have my own business website domain through another company and use their ecommerce. If I wanted to only use Shopify for my ecommerce, would the company that has my products on their site still get the commission on the products that are sold on my website because it is connected through my shopify account? Or does Shopify separate where the products are bought from so I will be able to get my full cut on the products that are sold on my personal website and the reduced cut from the products that are sold on an affiliate website?

Thanks so much,